Introduc)ontoR

KridsadakornChaichoompuGIGA-MedicalGenomics(BIO3)

UniversityofLiege

20/03/2017 KC-ULg 1

Basiccommands•  q() ToquitRenvironment•  x=5 Assignmentoperator•  y<-5 Assignmentoperator•  ls() TolistobjectsinRenvironment•  ?ls() Tocheckhowtouseafunc)on•  getwd() Togetaworkingdirectory•  setwd("New/Directory")

Tosetanewworkingdirectory•  save(x,y,file="mydata.RData")

TosaveobjectsastheRdatafile•  save.image(file="alldata.RData")

TosaveallobjectsastheRdatafile•  load("mydata.RData")

ToloadtheRdatafiletotheworkingspace

20/03/2017 KC-ULg 2

Arithme)coperators•  5+7 Addi)on •  8-3 Subtrac)on•  5*2 Mul)plica)on•  9/2 Division•  (8+3)*4 Parentheses•  2^4 Power•  exp(4) Exponen)alfunc)on•  log(8) NaturalLogarithm•  log10(8) Logarithminbase10•  pi Pinumber

20/03/2017 KC-ULg 3

LogicaloperatorsThevaluescanbeT,TRUE,F,FALSE•  5<6 lessthan•  5<=6 lessthanorequalto•  5>6 greaterthan•  5>=6 greaterthanorequalto•  5==6 exactlyequalto•  5!=6 notequalto•  !a NOTa•  a|b aORb•  a&b aANDb•  xor(a,b) aXORb•  isTRUE(a) testifXisTRUEExpressionstatement•  if(a==5&&b>5)•  if(a==5||b>5)

20/03/2017 KC-ULg 4

Basicdatatypesclass()-tocheckclassofobject•  Logical TRUE,T,FALSE,F

class(TRUE)•  Numeric 2.4,10,200

class(6.5)•  Integer 1L,0L,-7L

class(-8L)•  Complex 6+3i

class(6 + 3i)•  Character'hello',"I","like",'R'

class('hello')•  Factor

a = as.factor(1)a = as.factor('hello')class(a)

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VectorTocreatevectors•  a = c(1,2,0,6.6,-2.5) •  b = c("a","b","c") •  c = c(F,T,TRUE,FALSE)

Vectorsandoperators•  a + 5•  a * 2•  c & TRUE•  c | FALSE•  1:5 Vector of 1 to 5•  c(a,1:5) Concatenate 2 vectors

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MatrixTocreatematricesmatrix(vector,nrow=r,ncol=c,byrow=FALSE)•  a = matrix(1:12, nrow=3, byrow=F)•  b = matrix(1:12, nrow=3, byrow=T)•  c = matrix(runif(12,min=0,max=1), nrow=3, byrow=T)•  d = matrix(sample(c(TRUE,FALSE),12,replace=TRUE),

nrow=3, byrow=T)

Matricesandoperators•  a + 5•  a + b•  t(b) Transpose of matrix•  a * b Element-wise multiplication•  a %*% t(b) Matrix multiplication

20/03/2017 KC-ULg 7

Matrix(2)Toaccesselementsofmatrix•  a[1,1]•  a[,1]•  a[1,]•  a[,2:3]Tonamerowandcolumns•  colnames(a) = c("a","b","c","d")•  rownames(a) = c("1","2","3")Tocombine2matrices•  cbind(a,b)Combine by column•  rbind(a,b)Combine by row

20/03/2017 KC-ULg 8

Dataframe“data.frame”isthecollec)onsofvariableswhichsharemanyoftheproper)esofmatricesandoflists

Tocreatedata.frame•  x = c("Kris", "Jack", "Steve", NA)•  y = c(50,20,60,40)•  z = c(FALSE,TRUE,TRUE,FALSE)•  df = data.frame(x,y,z)•  colnames(df) <- c("name","paid","registered")

Usefulfunc)ons•  df$name•  is.na(df$name) Check all elements if they are NA?•  anyNA(df$name) Is there any NA?•  df$paid * 1.21•  dim(df) Check dimension•  df[which(df$name=="Kris"),] Get specific row

20/03/2017 KC-ULg 9

Dataframe(2)

Tonamerowandcolumns•  colnames(df) = c("1","2","3”)•  rownames(df) = c("a","b","c","d")Tocombine2matrices•  cbind(df,df) Combine by column•  rbind(df,df) Combine by row

20/03/2017 KC-ULg 10

List

Acollec)onofobjectswhichcanbeindifferentlength•  m = list(car=c("Toyota","Honda","Nissan"),age=c(23,67),single=TRUE)

Toaccessobjects•  m$car•  m$age•  m[[1]]•  m[[2]]

20/03/2017 KC-ULg 11

Conversionfunc)ons

•  as.matrix(df)•  as.data.frame(a)•  as.list(1:5)•  as.integer(1:5)•  as.logical(c(0,1,1,0))•  as.factor(1:5)

20/03/2017 KC-ULg 12

Concatena)onfunc)ons•  c() To combine vectors•  list() To combine lists•  cbind() To combine matrices and data frames by column•  rbind() To combine matrices and data frames by row•  paste("Hello","my","name","is","Kris")

To combine strings•  paste0("Hello","my","name","is","Kris")

To combine strings without spaceTricktodisplaytextonscreen•  str = paste("Hello","my","name","is","Kris","\n")•  cat(str) To display text•  print(str) To display all values as they are

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ControlFlow

•  if(condi)on)...•  if(condi)on)...else...

•  for(variableinsequence)...•  while(condi)on)...

•  break Tostopitera)on•  next Toskiptonextitera)on

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IFExamples:

age = 10if (age > 18){

cat("Old\n")}else{

cat("Young\n")}

age = 20if ((age>18) && (age<25)){

cat("Teenager\n")}else{

cat("Other type\n")}

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FOR

Examples:for (i in 1:10){cat(paste(i,"\n"))

}

name = c("Hello","my","name","is","Kris")for (i in name)cat(paste0(i," "))

20/03/2017 KC-ULg 16

WHILEExamples:i = 0while (i<5){

print(i)i = i+1

}

i = 0while (i<10){

if (i>5) nextprint(i)i = i+1

}

20/03/2017 KC-ULg 17

Importdelimitedtextfile•  TheformasedtextfilescanbeimportedtoRbythesefunc)ons:

–  Read.table()–  read.csv(),read.csv2()–  read.delim(),read.delim2()

•  Importantparameters:–  file:thenameofinputfile–  header:toindicatewhetherthefirstlinecontainsthenamesofthevariables

ornot–  sep=theseparatorcharacter

•  Trytoimportorange.csv

Downloadfromthecoursewebsite: hsp://www.montefiore.ulg.ac.be/~chaichoompu

•  Example:mydata=read.table(file="orange.csv",sep=",",header=TRUE)head(mydata)

20/03/2017 KC-ULg 18

Exportasdelimitedtextfile•  Youcanusethesefunc)onstoexporttofile

–  write.table(x,file="")–  write.csv()

•  Importantparameters:–  file:thenameofinputfile–  row.names:toindicatewhetherrownameswillbeexportedornot–  col.names:toindicatewhethercolumnnameswillbeexportedornot–  sep:theseparatorcharacter–  quote:toindicatewhethertextwillbequoted(“hello”)

•  Example:write.table(mydata,file="newfile.csv",quote=T,sep="\t",row.name=T,col.name=T)

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TextdisplayTodisplaytextonscreen•  print(x, ...)•  cat(...)

Concatenatevariables•  paste (...)•  paste0(...)Example:•  dd <- 28•  mm <- "October"•  yy <- 2016•  cat(paste0(dd,mm,yy))•  cat(paste(dd,mm,yy,sep="-"))

20/03/2017 KC-ULg 20

Plots•  Useplot()tocreateasimpleXYplot–  plot(rnorm(10))

•  Inthecompu)ngservers,weneedtosaveplotsasfilesandtransfertoalocalcomputertoview–  pdf(file="./xyplot.pdf")ècreateapdffileinthecurrentworkingdirectory

–  plot(rnorm(10))–  points(rnorm(2),col="red")èadd2reddotstotheplot–  dev.off()èclosethegraphicalsession,allgraphicalfunc)onscalledbeforedev.off()willbesavedtopdffile

•  Ralsosupportstheothertypesofgraphicalfiles–  Check:jpeg(),)ff(),png(),bmp()

20/03/2017 KC-ULg 21

Plovngformul)pledataseriesSingleline:

age=mydata$age[which(mydata$Tree==1)]cir=mydata$circumference[which(mydata$Tree==1)]plot(age,cir,type="o",xlab="Age",ylab="Circumference",col=1)

20/03/2017 KC-ULg 22

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Plovngformul)pledataseries(2)Addmorelines:

trees=sort(unique(mydata$Tree))subtrees=trees[-1]for (item in subtrees){ age=mydata$age[which(mydata$Tree==item)] cir=mydata$circumference[which(mydata$Tree==item)] lines(age,cir,col=item,type="o")}

20/03/2017 KC-ULg 23

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Mul)pleplotspar(mfrow=c(2,2))plot(rnorm(10),col="red")plot(rnorm(10),col="green")plot(rnorm(10),col="blue")plot(rnorm(10),col="pink")

20/03/2017 KC-ULg 24

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Wri)ngyourownfunc)onTodefinefunc)on:f1 <- function(param1, param2, ... ){

print(param1)return(param2)

}

NestedFunc)on:f2 <- function(p2,...){ f1 <- function(p1,...){

var1 <- log10(p1) return(var1) }

var2 <- f1(p2)return(var2)

}

20/03/2017 KC-ULg 25